This looks good Ben and Gavin. It's exactly what we need, and the JSON specs are something I can definitely produce from the models. Just make the specs for what you needs, and I'll make sure the modeling tools produce it. Chris On Nov 8, 2012, at 4:15 PM, Ben Bowen <[email protected]> wrote:

Not that I've given up on moving the little circles around on the web-page, but Gavin and I came up with a different version of what the reconciliation explorer might look like (attached). I leave it to your imagination to envision little tooltips on mouseover that have lots of info for the different reconciliations and new-tabs that open up when you click on a compound or reaction.

We have also begun to specify what the JSON object would look like. Next time I sit down to work on this, I'll make a toy JSON object and a web-page with the table and graphic. This probably won't be for several days; so if you want to add terms to the object or revise the "artists-rendering" please go crazy and put in whatever you want. It might be a good use of time to simultaneously, specify what the POST request will look like, where it will go, and what JSON object will be sent away from this page.

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On Mon, Nov 5, 2012 at 7:22 PM, Christopher Henry <[email protected]> wrote: Well, this gets more interesting when we lump in stats about how accuracy and model stats change when you select various solutions. Accepting a model modification is a trade off in a variety of ways: 1.) You may fix some errors but cause others 2.) You may reduce the number of active reactions in the model 3.) You may reduce the biomass reaction 4.) You may lose annotations

We need to report these stats in the interface so the user can see what they're trading off...

On Nov 5, 2012, at 5:47 PM, Gavin Price wrote:

...

will the model changes be clustered or linked somehow? I'm not quite sure how this interface makes displaying the results clearer/easier to understand - it looks like the model changes are arbitrarily placed.

-g

On 11/5/2012 3:43 PM, Ben Bowen wrote:

...

I just put together the beginnings of what the user interface might look like. You can check progress here:

http://metaboliteatlas.lbl.gov/~bpb/Demo/reconExplorer/reconciliationExplore...

Some imagination is still required, but the majority of the mechanics are in place.

Next, I'll import a toy json object that looks like what the gapfillGlobal will generate, and post a json object when your done selecting changes to the model.

----------------------------- Email: [email protected] Phone: (510) 214-6683 MS 977-221, Lawrence Berkeley Lab Web: ms.lbl.gov

On Sat, Nov 3, 2012 at 11:33 PM, Adam Paul Arkin <[email protected]> wrote: That is really nice.

Sent from my mobile device. Please excuse any seeming terseness or errors.

Adam Paul Arkin Dean A. Richard Newton Memorial Chair ------------------------------------- Director, Physical Biosciences Division E.O. Lawrence Berkeley National Laboratory

Professor, Department of Bioengineering University of California Berkeley, CA, 94720

PI and Co-Director, Virtual Institute of Microbial Stress and Survival, http://vimss.lbl.gov Director of Bioinformatics, The Joint Bioenergy Institute, http://jbei.lbl.gov Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org Head, Synthetic Biology, Physical Biosciences Division, Lawrence Berkeley National Laboratory

Office: 309B Hildebrand Hall (Berkeley Campus) Mailing address: E.O. Lawrence Berkeley National Laboratory 1 Cyclotron Road, MS Stanley-922 Berkeley, CA 94720

Contact: W: http://genomics.lbl.gov V: 510-495-2366 C: 510-206-1389 F: 510-486-6219

Assistant: Gwyneth A. Terry V: 510-495-2116 E: [email protected] -------------------------------------

On Nov 3, 2012, at 9:03 PM, Christopher Henry <[email protected]> wrote:

...

i love it!!!! We most definitely should do it. ASAP. Something like that could bring real shock and awe to the demo...

On Nov 3, 2012, at 8:59 PM, Ben Bowen wrote:

...

If you go to this link and click "next" http://elections.nytimes.com/2012/electoral-map there is a nice d3 visualization.

Instead of states: think media conditions (we have ~100) Instead of electoral votes for radius: think how many discrepancies were resolved Instead of dragging to explore voting outcomes: think which changes to the model you want to accept. Instead of tooltips with electoral votes: have option to select 1, 2, or 3 best modification to the model.

Add a button at the bottom for "commit" and get a nice, shiny new model to play with.

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<SpecificationsForReconciliationExplorer.pdf>